2O5J

Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the NTP substrate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

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This is version 1.3 of the entry. See complete history


Literature

Structural basis for substrate loading in bacterial RNA polymerase.

Vassylyev, D.G.Vassylyeva, M.N.Zhang, J.Palangat, M.Artsimovitch, I.Landick, R.

(2007) Nature 448: 163-168

  • DOI: https://doi.org/10.1038/nature05931
  • Primary Citation of Related Structures:  
    2O5J, 2PPB

  • PubMed Abstract: 

    The mechanism of substrate loading in multisubunit RNA polymerase is crucial for understanding the general principles of transcription yet remains hotly debated. Here we report the 3.0-A resolution structures of the Thermus thermophilus elongation complex (EC) with a non-hydrolysable substrate analogue, adenosine-5'-[(alpha,beta)-methyleno]-triphosphate (AMPcPP), and with AMPcPP plus the inhibitor streptolydigin. In the EC/AMPcPP structure, the substrate binds to the active ('insertion') site closed through refolding of the trigger loop (TL) into two alpha-helices. In contrast, the EC/AMPcPP/streptolydigin structure reveals an inactive ('preinsertion') substrate configuration stabilized by streptolydigin-induced displacement of the TL. Our structural and biochemical data suggest that refolding of the TL is vital for catalysis and have three main implications. First, despite differences in the details, the two-step preinsertion/insertion mechanism of substrate loading may be universal for all RNA polymerases. Second, freezing of the preinsertion state is an attractive target for the design of novel antibiotics. Last, the TL emerges as a prominent target whose refolding can be modulated by regulatory factors.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA. dmitry@uab.edu


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase alpha chainG [auth A],
H [auth B],
L [auth K],
M [auth L]
315Thermus thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5SHR6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SHR6
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta chainI [auth C],
N [auth M]
1,119Thermus thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE9
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta' chainJ [auth D],
O [auth N]
1,524Thermus thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity Groups  
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UniProt GroupQ8RQE8
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase omega chainK [auth E],
P [auth O]
99Thermus thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE7
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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3'A [auth G],
D [auth X]
23N/A
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3'B [auth H],
E [auth Y]
16N/A
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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3'C [auth I],
F [auth Z]
14N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

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U [auth D],
Z [auth N]
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
ZN
Query on ZN

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Q [auth D],
R [auth D],
V [auth N],
W [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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S [auth D],
T [auth D],
X [auth N],
Y [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.34α = 90
b = 152.34β = 90
c = 524.567γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description